At the moment we do almost (because we don't want any redirections to Wordpress through .htaccess at all at the moment) the same as you want.
Maybe I read/understand totally wrong what you mean.
(if so tell me in comment and I will delete this answer so no one will be confused)
At the moment we have 1 of our non Wordpress sites (which is running for years now) and installed Wordpress in subfolder of the root (public_html/wordpress-foldername).
Both have no connections to/with eachother and outher world does not know/see Wordpress.
As soon we have Wordpress ready to launch for public we will just copy .htaccess and index file to the root. (and leave Wordpress in subfolder ofcourse)
Telling the root index file where Wordpress folder is (after copying it) with this code:
require('./your-foldername/wp-blog-header.php'); moving also wp-config.php to the root and it will run as wished.
Moving wp-config.php to the root as soon it goes live and adding
(Some bad written plugins could make issue's because wp-config.php is not in the main Wordpress folder but that is already a reason not to use those that plugin)
No conflicts, no issues because Wordpress will act as it should and wanted. (Lot's of ppl have Wordpress in subfolder so it is excact the same, only difference is you work now with it and nobody knows it is in there)
Most hassle could be (will be in our case) redirecting "old url's to new url's" through .htaccess (need to have that part finished before you will launch Wordpress live ofcourse)
We also have at the moment Wordpress Search Engine Visibility OFF. We have taken precautions so no access and visibility for outherworld nor Google to Wordpress. (you could do with .htaccess and/or cPanel or DirectAdmin or other whatever other controllpanel)!
As soon .htaccess is redirecting all files/url's as should it is just a mather of 2 minits to launch, don't forget to tell Wordpress to have Search Engine Visibility enabled as soon it will be launched.Also go once in Back-end and go to General Settings and save once.
I hope this is some information you could use/ are looking for. And if you don't want to risk any, why not trying it out in a sandbox first.
Note:About the possible issue's Mark Kaplun is fearing for, there is non because the active site is not pointing to Wordpress and visa versa, we did this once before and working at this project now also for some weeks and did not have 1 issue. Sorry Mark no offence meant but imho there is/can't be even 1 issue. Only thing which could be a hassle is making a sitemap as long it is in development state so don't even do it at that point.